Pakistan made an official protest to India on Friday after detaining a man it says is an Indian spy who illegally entered the country and was captured on Thursday in the violence-plagued province of Baluchistan.
India's foreign ministry confirmed that Pakistan's foreign secretary had taken up the matter with the Indian High Commissioner in Islamabad but denied the man was a spy.
"The said individual has no link with the government since his premature retirement from the Indian Navy," the foreign ministry said in a statement. "We have sought consular access to him."
Tensions are already high between the nuclear-armed nations after India blamed Pakistan-based militants for a January attack on the Indian air base in Pathankot in which seven military personnel were killed.
"(Pakistan) conveyed our protest and deep concern on the illegal entry into Pakistan by a RAW officer and his involvement in subversive activities in Baluchistan and Karachi," Pakistan's foreign ministry said in a statement on Friday, referring to a message conveyed to India's ambassador.
The Research and Analysis Wing (RAW) is India's main external intelligence agency.
Pakistan believes that India is supporting separatists in the resource-rich Baluchistan province, as well as militants fighting the state from the lawless tribal areas. It also sees India as fuelling strife in the volatile city of Karachi.
India denies any such interference and has itself accused Pakistan of backing militants fighting Indian security forces in its part of the divided Kashmir region, of helping militants to launch attacks elsewhere in India and backing the Taliban in Afghanistan.
Pakistan says it only offers diplomatic support to the Muslim people of Kashmir living under what it says heavy-handed Indian rule. It denies backing militant attacks in India.
A Pakistani military official in Baluchistan told Reuters the alleged RAW spy was an Indian navy officer. Another Pakistani official gave the same information.
Both declined to be identified because they were not authorised to give details of the incident to the media.
One of the officials said the man had been moved to Islamabad for interrogation.
The neighbouring countries have fought three wars since 1947, two of them over Kashmir, which they both claim in full but rule in part.
Baluchistan's provincial interior minister, Mir Sarfaraz Bugti, told reporters that the arrest "proved Indian involvement" in his province.
Last year Pakistan's defence minister Khawaja Asif said that the RAW was determined on annihilating Pakistan.
"RAW has been formed to undo Pakistan and to wipe Pakistan off the map," Asif said in a television interview.
Pakistan Prime Minister Nawaz Sharif has sought to improve ties with India since his election in 2013, but his efforts are widely considered to have caused friction with the army, which sees relations with India as its domain.
Last December Prime Minister Narendra Modi made a surprise stopover in Pakistan to meet Sharif, the first visit by an Indian premier in more than a decade, raising hopes that stop-start negotiations might finally make progress after decades of hostility.